Comparative protein structure modeling by iterative alignment, model building and model assessment.
By Bino John, Andrej Sali. Nucleic Acids Research, 2003
341 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/1ec78cb22aec5f80d28006e02c4ffffb8bc2bf3c
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Ben M. Webb
- Andrej Sali
- Yang Zhang
- Min-Yi Shen
- David Eramian
- Narayanan Eswar
- Ursula Pieper
- Mallur Srivatsan Madhusudhan
In Molecular Biology
- Ben M. Webb
- Andrej Sali
- Yang Zhang
- Min-Yi Shen
- David Eramian
- Narayanan Eswar
- Torsten Schwede
- Ursula Pieper
Citations in the corpus
- Evaluating protein structures determined by structural genomics consortia (2006, background): “The resulting structural inaccuracies can result in poor global or site-specific structural quality assessment scores and/or high conformational energies.(22,23) The pro-”
- Protein structure modeling with MODELLER. (2014, methodology): “DOPE score and the energy profile, but also the GA341 assessment score(25,26) and an estimate of the Cα RMSD and native overlap between the model and its hypothetical native structure, using the TSVMod method(27); native overlap is defined as the fraction of Cα atoms in the model that are within 3.”
- 3DRobot: automated generation of diverse and well-packed protein structure decoys (2016, methodology): “, 1997), homology modeling by Modeller (John and Sali, 2003), and multiple threading assembly simulation from I-TASSER (Wu et al.”
- Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “The second way of improving the alignment is to iteratively modify those regions in the alignment that correspond to predicted errors in the model (Sanchez and Sali, 1997a, 1997b; John and Sali, 2003).”
- Statistical potential for assessment and prediction of protein structures (2006, methodology): “…function determined and computationally predicted protein structures (Sippl 1993b; DeBolt and Skolnick 1996; Gatchell et al. 2000; Melo et al. 2002; John and Sali 2003; Wang et al. 2004; Topf and Sali 2005; Topf et al. 2006), ab initio protein structure prediction and Crippen 1992; Sippl and…”
- Comparative Protein Structure Modeling Using MODELLER (2007, methodology): “The second way of improving the alignment is to iteratively modify those regions in the alignment that correspond to predicted errors in the model (Sanchez and Sali, 1997a,b; John and Sali, 2003).”
- Alignment of protein sequences by their profiles (2004, background): “2000; Blake and Cohen 2001; Panchenko 2003; Sadreyev and Grishin 2003), as well as optimized the alignment accuracy for protein structure prediction (Jaroszewski et al. 2000; John and Sali 2003).”
- Comparative Protein Structure Modeling Using Modeller (2006, methodology): “Although this procedure can be time consuming, it can significantly improve the accuracy of the resulting comparative models in difficult cases (John and Sali, 2003).”
- Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “The second way of improving the alignment is to iteratively modify those regions in the alignment that correspond to predicted errors in the model (Sanchez and Sali, 1997a, 1997b; John and Sali, 2003).”